"I'm worried about the inhalation of a product and the risks associated with that. I'm worried about the perception that somehow there's no risks associated with youth use of the product," Gottlieb said in an interview with CNBC on Thursday.

Previous studies have looked at the risks of occasional marijuana use, but regular use is increasingly common as it's legalized, he said. "I think that's going to create a different set of risks," he said.

The rising popularity of weed among adults appears to be filtering down to younger generations. Nearly one-quarter of teens are now using pot and fewer students disapprove of the drug, according to the annual "Monitoring the Future" survey conducted by the University of Michigan. The number of high school students seeing "great risk" in marijuana use dropped to 14.1 percent last year from 17.1 percent in 2016, according to the report.

"I think we all need to be deeply concerned about that in the same way we're deeply concerned about youth access to e-cigarettes and nicotine," Gottlieb said. "We should be even more concerned about youth access to marijuana and cannabis."

Gottlieb's comments come after a wild three days of trading for shares of Canadian pot grower Tilray. The stock shot up more than 56 percent on Tuesday and Wednesday before dropping about 20 percent on Thursday. Tilray shares have surged nearly 400 percent over the past month.

And Tilray isn't the only popular pot stock. Shares of Cronos are up about 80 percent in the past month, while shares of Aurora Cannabis have risen 55 percent in that time period. The ETFMG Alternative Harvest exchange-traded fund — which tracks the performance of marijuana shares — has shot up 46.2 percent in the past 30 days.

Tilray's rise pushed the company's market cap to around $16 billion, up sharply from $2.1 billion after its IPO. Aurora's market cap, meanwhile has jumped to about C$11.2 billion from just under C$5 billion earlier this month. Cronos' market value is above C$3.1 billion, up from about C$2.5 billion earlier in September.

Gottlieb called teen e-cigarette use an "epidemic" last week and threatened to pull e-cigarettes from shelves if manufacturers do not control teen use. The agency is specifically ordering five brands — Juul, British American Tobacco's Vuse, Altria's MarkTen, Imperial Brands' Blu E-cigs and Japan Tobacco's Logic — to submit plans within 60 days detailing how they will prevent teens from using their products.

Additionally, the agency is investigating whether manufacturers' online shops are being used for "straw" purchases, where buyers resell products to minors. If the FDA identifies problems, it can take both civil and criminal actions. It also warned more than 1,300 retailers for illegally selling e-cigarettes to minors.

The 2017 Michigan report indicates that teen marijuana use could continue to grow as more states legalize the drug, according to the study's authors.

Funded by the National Institute on Drug Abuse and National Institutes of Health, the study provides the most comprehensive look at drug use among young adults in the U.S.